chr1-119816127-C-T

Position:

• chr1-119816127-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0198 in 152,186 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.020 (42 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0198 (3009/152186) while in subpopulation AFR AF= 0.0362 (1501/41510). AF 95% confidence interval is 0.0346. There are 42 homozygotes in gnomad4. There are 1426 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 42 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0198 AC: 3005 AN: 152068 Hom.: 42 Cov.: 32

Gnomad AFR AF: 0.0362

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0147

Gnomad ASJ AF: 0.0401

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0104

Gnomad FIN AF: 0.00170

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0132

Gnomad OTH AF: 0.0158

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0198 AC: 3009 AN: 152186 Hom.: 42 Cov.: 32 AF XY: 0.0192 AC XY: 1426 AN XY: 74388

Gnomad4 AFR AF: 0.0362

Gnomad4 AMR AF: 0.0147

Gnomad4 ASJ AF: 0.0401

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0108

Gnomad4 FIN AF: 0.00170

Gnomad4 NFE AF: 0.0132

Gnomad4 OTH AF: 0.0156

Alfa AF: 0.0163 Hom.: 7

Bravo AF: 0.0217

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.8
DANN	Benign	0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10494232; hg19: chr1-120358750;